Gene expression profiling of Phalaenopsis orchids
Ontology highlight
ABSTRACT:
ORGANISM(S): Phalaenopsis aphrodite
PROVIDER: GSE29910 | GEO | 2015/06/02
SECONDARY ACCESSION(S): PRJNA140823
REPOSITORIES: GEO
Similar Datasets
Project description:To identify genes affected by Pha21, Pha21 was transiently overexpressed in leaves of P. aphrodite by agroinfiltration. The leaves of P. aphrodite infiltrated with agrobacterium carrying empty vector (without Pha21) was used as a control. Transcriptional profiling was analyzed using a customized oligonucleotide array with RNA extracted from Pha21 and empty vector overexpressed leaves of P. aphrodite. The sequences used for probe design were collected from the Orchidstra 2.0 database (http://orchidstra2.abrc.sinica.edu.tw/orchidstra2/index.php). Totally, 42,973 probes were designed on this oligonucleotide array.
2017-01-07 | GSE93247 | GEO
Project description:To identify genes affected by Pha13, Pha13 was transiently overexpressed in leaves of P. aphrodite by agroinfiltration. The leaves of P. aphrodite infiltrated with agrobacterium carrying empty vector (without Pha13) was used as a control. Transcriptional profiling was analyzed using a customized oligonucleotide array with RNA extracted from Pha13 and empty vector overexpressed leaves of P. aphrodite. The sequences used for probe design were collected from the Orchidstra 2.0 database (http://orchidstra2.abrc.sinica.edu.tw/orchidstra2/index.php). Totally, 42,973 probes were designed on this oligonucleotide array.
2017-01-07 | GSE93246 | GEO
Project description:The aim of this experiment was to compare the transciptome of the fall armyworm (Spodoptera frugiperda) strain SUS (a laboratory insecticide-susceptible standard) with organophosphate (OP) and pyrethroid (PYR) resistant strains were collected in cornfields located in Minas Gerais and Mato Grosso States, Brazil, in 2008 and maintained in the laboratory under selection with chlorpyrifos (at increasing discriminating doses from 100 up to 400 µg of insecticide/g of insect in a topical bioassay) or lambda-cyhalothrin (from 8.4 up to 27 µg of insecticide/g of insect) respectively The custom microarray used in this study was designed using the Agilent eArray platform (Agilent Technologies). A SurePrint HD (8×15k) expression array was designed using the base composition and the best probe methodologies to design sense orientation 60-mer probes with a 3′ bias. The FAW EST database (SPODOBASE) was used as the reference transcriptome (Negre, Hotelier et al. 2006). These sequences are derived from 8 cDNA libraries as follows: Sf1F: Fat body, Sf1H: Hemocyte, Sf1M: Midgut, Sf1P: Pool of various tissues, Sf2H: Immune Challenged hemocytes, Sf2L: Sf21 Cell lines sequences, Sf2M: Xenobiotic Induced Midgut and Sf9L: Sf9 cell lines sequences. All assembled contigs and singlets were kindly sent by the website maintainers. The BLAST2GO software v.2.3.1 (http://www.blast2go.org) was used to annotate the EST database. 60-mer probes were designed for all 7,552 assembled contigs and 5,519 annotated singlets (BlastX), totaling 13,071 sequences. For contigs encoding detoxification enzymes (P450s, GSTs and CEs) three probes were designed. Additional probe groups for 15 control genes were also included. For reference all sequences are included in the zip file with array data. References: Negre, V., T. Hotelier, et al. (2006). "SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera." BMC Bioinformatics 7: 322.
2013-08-01 | GSE43295 | GEO
Project description:The aim of this experiment was to compare the transciptome of the fall armyworm (Spodoptera frugiperda) strain SUS (a laboratory insecticide-susceptible standard) with organophosphate (OP) and pyrethroid (PYR) resistant strains were collected in cornfields located in Minas Gerais and Mato Grosso States, Brazil, in 2008 and maintained in the laboratory under selection with chlorpyrifos (at increasing discriminating doses from 100 up to 400 M-BM-5g of insecticide/g of insect in a topical bioassay) or lambda-cyhalothrin (from 8.4 up to 27 M-BM-5g of insecticide/g of insect) respectively The custom microarray used in this study was designed using the Agilent eArray platform (Agilent Technologies). A SurePrint HD (8M-CM-^W15k) expression array was designed using the base composition and the best probe methodologies to design sense orientation 60-mer probes with a 3M-bM-^@M-2 bias. The FAW EST database (SPODOBASE) was used as the reference transcriptome (Negre, Hotelier et al. 2006). These sequences are derived from 8 cDNA libraries as follows: Sf1F: Fat body, Sf1H: Hemocyte, Sf1M: Midgut, Sf1P: Pool of various tissues, Sf2H: Immune Challenged hemocytes, Sf2L: Sf21 Cell lines sequences, Sf2M: Xenobiotic Induced Midgut and Sf9L: Sf9 cell lines sequences. All assembled contigs and singlets were kindly sent by the website maintainers. The BLAST2GO software v.2.3.1 (http://www.blast2go.org) was used to annotate the EST database. 60-mer probes were designed for all 7,552 assembled contigs and 5,519 annotated singlets (BlastX), totaling 13,071 sequences. For contigs encoding detoxification enzymes (P450s, GSTs and CEs) three probes were designed. Additional probe groups for 15 control genes were also included. For reference all sequences are included in the zip file with array data. References: Negre, V., T. Hotelier, et al. (2006). "SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera." BMC Bioinformatics 7: 322. Two-condition experiment. Slide 1: SUS vs. OP S. fugiperda strains. Slide 2: SUS vs. PYR S. fugiperda strains. Biological replicates: 4 pools of RNA extracted from four pools of 5 second instar larvae. Technical Replicates: None, the biological replicates incorporated a dye swap. Total replication: four replicates for each strain.
2013-08-01 | E-GEOD-43295 | biostudies-arrayexpress
Project description:BACKGROUND: In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcripts for identification of their human homologues. RESULT: The full-insert sequences of 512 cDNA clones were determined. Ultimately we found 302 non-redundant cDNAs carrying open reading frames of 300 bp-length or longer. Among them, 89 cDNAs were found not to be annotated previously in the Ensembl human database. After searching against the Ensembl mouse database, we also found 69 putative coding sequences have no homologous cDNAs in the annotated human and mouse genome sequences in Ensembl.We subsequently designed a DNA microarray including 396 non-redundant cDNAs (with and without open reading frames) to examine the expression of the full-sequenced genes. With the testicular probe and a mixture of probes of 10 other tissues, 316 of 332 effective spots showed intense hybridized signals and 75 cDNAs were shown to be expressed very highly in the cynomolgus monkey testis, but not ubiquitously. CONCLUSIONS: In this report, we determined 302 full-insert sequences of cynomolgus monkey cDNAs with enough length of open reading frames to discover novel transcripts as human homologues. Among 302 cDNA sequences, human homologues of 89 cDNAs have not been predicted in the annotated human genome sequence in the Ensembl. Additionally, we identified 75 dominantly expressed genes in testis among the full-sequenced clones by using a DNA microarray. Our cDNA clones and analytical results will be valuable resources for future functional genomic studies. Keywords: other
2003-07-16 | GSE513 | GEO
Project description:Orchidaceae are renowned for their spectacular flowers as well as other reproductive and ecological adaptations. After the genome of the tropical epiphytic orchid Phalaenopsis equestris was sequenced, we combined Trinity data for de novo assembly and Illumina HiSeq1500 data for RNA-Seq analysis to characterize the transcriptomes of four different organs for a better understanding of the molecular mechanisms driving these characteristics. We present four de novo assembled transcripts reconstructed from RNA collected from the root, stem, leaf, and flower of Phalaenopsis equestris. These sets of transcripts greatly enrich the available data for Phalaenopsis equestris. Here, we present two databases, and each dataset allows for a different type of search for candidate homologues. The first dataset consists of the sets of assembled unigenes, which enable a sequence-based search. A comprehensive analysis of the assembled unigenes revealed the unigenes from root, stem, leaf, and flower with high e-values aligned versus the Nr, Swiss-Port, KEGG, COG, and GO database, respectively. This analysis enabled the production of a second database, which includes sequences correlated with annotated transcript names as well as the confidence of the best hit from BLAST.
2018-06-30 | GSE70411 | GEO
Project description:The NimbleGen array contains 387,000 46~50-mer oligos, including 377,230 salmonella probes whose sequences only hit genome once. The probes were designed based on Salmonella typhimurium LT2 (NC_003197) genome, with a moving window of about 12 bases. Raw intensities were normalized by the median intensity in each channel and the ratios were calculated by log base 2 (hns-bound DNA / genomic DNA) after the normalization. Keywords: ChIP-chip
2006-05-23 | GSE4879 | GEO
Project description:For identification of genes up-regulated in RCc3:OsNAC5, GOS2:OsNAC5 plants, total RNA (100 μg) was prepared from root tissues of 14-d-old transgenic and non-transgenic rice seedlings (Oryza sativa cv Nipponbare) grown under normal growth conditions. Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in RCc3:OsNAC5, GOS2:OsNAC5 and Non-transgenic plants. Cy3-labeled target cDNA fragments were synthesized using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.
2012-03-01 | E-GEOD-31856 | biostudies-arrayexpress
Project description:For identification of genes up-regulated in RCc3:OsNAC1, GOS2:OsNAC1 plants, total RNA (100 μg) was prepared from root tissues of 14-d-old transgenic and non-transgenic rice seedlings (Oryza sativa cv Nipponbare) grown under normal growth conditions. Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 °C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in RCc3:OsNAC1, GOS2:OsNAC1 and Non-transgenic plants. Cy3-labeled target cDNA fragments were synthesized using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.
2012-03-01 | E-GEOD-31855 | biostudies-arrayexpress